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Plot genome track data

Project description

gtracks

Plot genome track data from bigWig files. Powered by pyGenomeTracks.

Installation

pip3 install gtracks

or

pip3 install --user gtracks

Examples

An example bigwig file with ATAC-seq data from the insulin region is included. You can generate a test plot like this:

gtracks INS-IGF2 test.png

test plot

You can plot your own tracks over other genomic regions by providing more positional arguments: a region or gene name and paths to one or more bigWig files. The file type of the plot will be determined by the output file extension.

gtracks chr11:2150341-2182439 track1.bw track2.bw output.pdf
gtracks INS track1.bw track2.bw output.svg

Modifying the gene annotations track

GRCh37/hg19 gene annotations are used by default, but you can plot GRCh38/hg38 genes by adding --genes GRCh38 or --genes hg38. You can use your own gene annotations file (BED or BED12 format) by providing --genes <path/to/genes.bed.gz>.

You may want to add more rows to the genes track. You can do this using the --genes-height and --gene-rows options.

gtracks INS test-genes.png --genes-height 6 --gene-rows 6

test plot with more gene rows

Changing the color palette

You can change the color palette for bigWig tracks using the --color-palette option.

gtracks INS track1.bw track2.bw track3.bw output.pdf --color-palette "#color1" "#color2" "#color3"

Setting y-axis height

By default, tracks have different y-axis heights depending on signal height. You can set a uniform y-axis height for all tracks using the --max option.

gtracks INS track1.bw track2.bw track3.bw output.pdf --max 400

For more command-line options, see the usage page below.

Environment variables

If you want to use your own bigWig files but don't want to write out their paths every time you run gtracks, you can set your own default tracks using the environment variable GTRACKS_TRACKS.

export GTRACKS_TRACKS=track1.bw,track2.bw,track3.bw
gtracks output.pdf

You can also change the default gene annotations file and color palette using environment variables GTRACKS_GENES_PATH and GTRACKS_COLOR_PALETTE.

export GTRACKS_GENES_PATH=path/to/genes.bed.gz
export GTRACKS_COLOR_PALETTE="#color1,#color2,#color3"
gtracks output.pdf

Usage

usage: gtracks [-h] [--genes <{path/to/genes.bed.gz,GRCh37,GRCh38,hg19,hg38}>]
               [--color-palette <#color> [<#color> ...]] [--max <float>]
               [--tmp-dir <temp/file/dir>] [--width <int>]
               [--genes-height <int>] [--gene-rows <int>]
               <{chr:start-end,GENE}> [<track.bw> [<track.bw> ...]]
               <path/to/output.{pdf,png,svg}>

Plot bigWig signal tracks and gene annotations in a genomic region

positional arguments:
  <{chr:start-end,GENE}>
                        coordinates or gene name to plot
  <track.bw>            bigWig files containing tracks
  <path/to/output.{pdf,png,svg}>
                        path to output file

optional arguments:
  -h, --help            show this help message and exit
  --genes <{path/to/genes.bed.gz,GRCh37,GRCh38,hg19,hg38}>
                        compressed 6-column BED file or 12-column BED12 file
                        containing gene annotations. Alternatively, providing
                        a genome identifier will use one of the included gene
                        tracks. (default: GRCh37)
  --color-palette <#color> [<#color> ...]
                        color pallete for tracks
  --max <float>         max value of y-axis
  --tmp-dir <temp/file/dir>
                        directory for temporary files
  --width <int>         width of plot in cm (default: 40)
  --genes-height <int>  height of genes track (default: 2)
  --gene-rows <int>     number of gene rows (default: 1)

Project details


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